Re: problem at maintaining geometry coordinate

From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Mon Aug 23 2010 - 23:02:54 CDT

On Mon, Aug 23, 2010 at 6:11 PM, <ehenriques_at_qui.uc.pt> wrote:

> Quoting Kwee Hong <joyssstan0202_at_gmail.com>:
>
> ... I've done some adjustment to the parameter file (
>> par_all22_prot.inp <http://birg1.fbb.utm.my/joyce/modpar.html>).
>> ...
>> ...The Cd-S bond length has
>>
>> become more than 0.6nm. According to experiment, the bond length and bond
>> angle should be as follow:
>>
>>
>> Cd-S(terminal) 0.2467nm
>> Cd-S(bridging) 0.2560nm
>>
>> S-CD-S 109.5
>> Cd-S-C 95.5
>>
>>
> Hi,
>
>
> To start with, in your "modpar" file you set the force constant of
> Cd-S(...) bond(s) to 0.00, so no wonder you got such big 'deviations' [look
> for the physical meaning of each term of the force-field formula in the
> literature].

I actually ran another simulation with the following adjustment in the
parameter file:

CAD SS 127.000 2.467
CAD S1 127.000 2.56

The force constant was taken from a literature which employ Charmm22, too.
With this parameter, all the cadmium eventually clamped together at a single
point even at the minimization stage. So, does this mean that I would need
to adjust the force constant to get the desired coordination geometry? What
would be the thumb of rule in adjusting the force constant so that I can
eventually obtain the desired coordination geometry.

There is another thing that puzzle me, out from the papers which I refer to
in simulating the metallothionein, most of them just include the bond length
and bond angle in their publication without stating the force constant they
used in the simulation. Why does this happen since force constant affects so
much in getting the right coordination geometry?

> Besides, I don't see any entry in the "modpar" for bond angles or dihedrals
> around the CAD atom. So, did you really set a formal bond between the
> cadmium and the sulfur(s) in your topology file?!? [if you did, the program
> should complain about the absence of the angle and dihedral terms...]
>

Elsa, you have pointed out something which have puzzled me, too. I actually
just patch the CAD-S bond. I believe this is not the formal bond right? So
this would be the reason the program did not complain the angle and dihedral
terms?

I actually have problem in defining the connection between the cysteinyl
thiols and cadmium correctly. One cadmium is coordinated/bound to 4
cysteines. There is 9 cysteines in the protein to coordinate 3 cadmium ions--0016e64717acecd2b3048e89d6b4--

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